With sea-rise trends appearing to accelerate, Waterkeeper and its hired science guns argue the county will be pouring nearly $1 billion into rehabbing plants likely to be incapacitated long before the 50-year life span expected of big-ticket public works projects. They believe the best choice is to move plants to more protected inland sites. At the least, they argue they should be built higher and much stronger, a choice they say the county hasn’t realistically assessed that would likely add dramatically to costs.

Of particular concern: a nearly $600 million reconstruction of the trouble-prone plant on Virginia Key, where four spills over just three months in 2011 dumped some 19 million gallons of waste water into Biscayne Bay.

Even under conservative projections, the site is vulnerable, a sandy island fronting the Atlantic Ocean where beaches and mangroves could disappear within 35 years. “Why do we want to think about upgrading that plant?’’ Wanless said.

Doug Yoder, deputy director of the water and sewer department, defended the county plan as a cost-effective approach to resolving the most pressing concerns — orders by the EPA, U.S. Department of Justice and Florida Department of Environmental Protection to repair a system that has spilled 47 million gallons of sewage in the past few years.

With so much uncertainty over timing — differences in projected impacts span decades — Yoder said it didn’t make financial sense to abandon the most critical and expensive components. Moving the Virginia Key plant alone, Yoder said, could run $3 billion — five times the cost of an upgrade. Another plant also could be built in 20 or 30 years if needed, he said.

“If you put aside storm surge and just look at the groundwater levels that will result, that plant is going to still be dry after a lot of the rest of Virginia Key, South Beach and Key Biscayne would be pretty much at ground water level,’’ Yoder said. By then, the county would have gotten its money’s worth out of upgrades and sewage flow might be reduced anyway if people are forced to retreat from flooded areas.

Yoder disputed charges of ignoring climate risks, saying the issues were beyond the scope of a legal agreement to fix existing problems.

He insisted the county would evaluate threats and beef up vulnerable components as it begins the formal design process. Existing building codes, the toughest in the nation, also may call for added protections, such as surge barriers or pumps, he said.

The county, for instance, elevated and strengthened a building housing backup electrical systems for a recent $600 million project at the south plant — a site that lost power for two weeks after Hurricane Andrew in 1992.

The EPA and DEP declined to discuss ongoing litigation.

Pushing regulators

Davina Marraccini, an EPA spokeswoman, said it was important for utilities to consider “all available information — including statistical data about population growth and weather patterns — and apply sound engineering practices.’’ DEP spokeswoman Dee Ann Miller said her agency “certainly appreciates the concerns’’ raised by Waterkeeper.

Attorneys for Waterkeeper, which is seeking to join the EPA action as an intervener and has filed a separate citizen’s suit as well, are pushing regulators to exercise stronger oversight of a county they argue has a history of penny-wise, pound-foolish decisions. Despite two decrees in the 1980s and 1990s, the sewage system has slipped into such disrepair that the department director, John Renfrow, last year likened it to “being held together by chewing gum.’’